R Markdown documents are converted to PDF by first converting to a TeX file and then calling the LaTeX engine to convert to PDF. By default, this TeX file is removed, however if you want to keep it (e.g., for an article submission), you can specify the keeptex option. Today, I will be talking about how to generate a nice pdf report with text, code, plots, and formulas using R markdown. For those of you who are in a hurry, you will find the entire code at the end of this post. Simply skip to Step 2 to learn how to convert it into pdf. Once again, I will explain how to do this in command line. R markdown does not create a pdf file #1285. Bdeepthi opened this issue Mar 11, 2018 59 comments Milestone. Copy link bdeepthi commented Mar 11. R Markdown Cheat Sheet learn more at rmarkdown.rstudio.com rmarkdown 0.2.50 Updated: 8/14 1. Workflow R Markdown is a format for writing reproducible, dynamic reports with R. Use it to embed R code and results into slideshows, pdfs, html documents, Word files and more. To make a report. In this tutorial, we will render or knit an R Markdown document to a web friendly, html format using the R knitr package. Knitr can be used to convert R Markdown files to many different formats including: html, pdf, GitHub markdown (.md ) and more.
R/printers.RFunction used to render flextable in knitr/rmarkdown documents.
You should not call this method directly. This function is used by the knitrpackage to automatically display a flextable in an 'R Markdown' document froma chunk. However, it is recommended to read its documentation in order to getfamiliar with the different options available.
HTML, Word, PowerPoint and PDF outputs are supported.
Table captioning is a flextable feature compatible with R Markdowndocuments. The feature is available for HTML, PDF and Word documents.Compatibility with the 'bookdown' package is also ensured, including theability to produce captions so that they can be used in cross-referencing.
Arguments
| x | a |
|---|---|
| ... | further arguments, not used. |
Note
Supported formats require someminimum pandoc versions:
| Output format | pandoc minimal version |
| HTML | >= 1.12 |
| Word (docx) | >= 2.0 |
| PowerPoint (pptx) | >= 2.4 |
| >= 1.12 |
Chunk options
Some features, often specific to an output format, are available to help youconfigure some global settings relatve to the table output. knitr's chunk optionsare to be used to change the default settings:
| chunk option | property | default value | HTML | docx | pptx | |
| ft.align | flextable alignment, supported values are 'left', 'center' and 'right' | 'center' | yes | yes | yes | no |
| ft.shadow | HTML option, disable shadow dom (set to FALSE) for pagedown. | TRUE | yes | no | no | no |
| ft.split | Word option 'Allow row to break across pages' can be activated when TRUE. | FALSE | no | yes | no | no |
| ft.tabcolsep | space between the text and the left/right border of its containing cell | 8.0 | no | no | yes | no |
| ft.arraystretch | height of each row relative to its default height | 1.5 | no | no | yes | no |
| ft.left | left coordinates in inches | 1.0 | no | no | no | yes |
| ft.top | top coordinates in inches | 2.0 | no | no | no | yes |
Table caption
Captions can be defined in two ways.
The first is with the set_caption function. If it is used,the other method will be ignored. The second method is by usingknitr chunk option tab.cap.
If set_caption function is not used, caption identifier will beread from knitr's chunk option tab.id or label if in a bookdown(this is to respect the bookdown standards).
R Markdown Pdf Output
tab.id='my_id' or label='my_id'
Word output provide more options such as ability to choose the prefix for numbering chunk forexample. The table below expose these options:
| chunk option | purpose | rmarkdown | bookdown |
| tab.cap.style | (Word only) style name to use for table captions | yes | yes |
| tab.cap.pre | (Word only) Prefix for numbering chunk (default to 'Table') | yes | yes |
| tab.cap.sep | (Word only) Suffix for numbering chunk (default to ': ') | yes | yes |
| tab.cap | Caption label | yes | yes |
| tab.id | Caption reference unique identifier | yes | no |
| label | Caption reference unique identifier | no | yes |
HTML output
HTML output is using shadow dom to encapsule the tableinto an isolated part of the page so that no clash happenswith styles. Some output may not support this feature. To ourknowledge, only the pagedown output is concerned.Use knitr chunk option ft.shadow=FALSE to disable shadow dom.
PDF output
Some features are not implemented in PDF due to technicalinfeasibility. These are the padding, line_spacing andheight properties.
PowerPoint output
Auto-adjust Layout is not available for PowerPoint.
Also images cannot be integrated into tables with the PowerPoint format.
See also
Other flextable print function: as_raster(),flextable_to_rmd(),htmltools_value(),plot.flextable(),print.flextable(),save_as_docx(),save_as_html(),save_as_image(),save_as_pptx()
Examples
Table of Contents
R Packages
R Markdown Custom Formats: https://blog.rstudio.org/2016/03/21/r-markdown-custom-formats/
tufte— Documents in the style of Edward Tufterticles— Formats for creating LaTeX based journal articlesrmdformats— Formats for creating HTML documents
markdowntemplates: A collection of alternate R markdown templates https://github.com/hrbrmstr/markdowntemplatesthesisdown: An updated R Markdown thesis template using the bookdown package https://github.com/ismayc/thesisdownprettydoc: Creating Pretty HTML From R Markdown http://yixuan.cos.name/prettydoc/rmdTemplatesR package containing a collection of Rmarkdown templates https://github.com/Pakillo/rmdTemplatesmanuscriptPackageTemplate for writing manuscripts as an R package https://github.com/jhollist/manuscriptPackagetemplateA template for my research projects, based on the R package structure https://github.com/cboettig/templatermarkdown-website-template: Template for creating your website with R markdown. https://github.com/privefl/rmarkdown-website-template
R Markdown Tutorial
User defined
- Simple template for scientific manuscripts in R markdown: http://www.petrkeil.com/?p=2401
- An R Markdown Template for Academic Manuscripts: http://svmiller.com/blog/2016/02/svm-r-markdown-manuscript/
rmarkdown-article-templateA personal template for Rmarkdown https://github.com/danilofreire/rmarkdown-article-template- R Markdown template for CSUN Master Thesis: https://github.com/carlganz/CSUNtemplate
uiucthemes: RMarkdown Templates for UIUC Theme-Oriented Documents (e.g. UIUC Beamer) https://github.com/coatless/uiucthemesucbthesis: Latex, Knitr, and RMarkdown templates for UC Berkeley’s graduate thesis.svm-r-markdown-templates: R Markdown templates for academic manuscripts, beamer presentations, and syllabi https://github.com/svmiller/svm-r-markdown-templates
R Markdown Pdf Template
Chinese
R Markdown Pdf Latex
Template for creating Chinese beamer & PDF on Windows: https://github.com/BruceZhaoR/Zh-beamer